Brandon Savage has his own response to the "comments are harmful" post over on the PHP in Action blog:

There's a lot of good advice, especially about writing clean code. But the article fails to address a good number of really critical details and to some degree misses the point of Eli's article.

He mentions these points - the value of writing comments before hand, the usefulness of descriptive comments, how they can be used as a todo pointing to future development and using them to share the knowledge and let other people in on what you're thinking.